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jasperlinthorst / reveal

Graph based multi genome aligner
MIT License
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reveal realign - muscle fails #26

Open ChriKub opened 5 years ago

ChriKub commented 5 years ago

Hi, I'm using reveal realign with muscle to realign bubbles in a graph. reveal realign --64 --method muscle --all --maxsize 5000 -o $output $input At some point during the realignment it fails: 10/03/2018 01:04:06 PM Realigning bubble between <431323> and <99201>, 2 alleles, with muscle (max size 10bp, in nodes=2). Traceback (most recent call last): File "/ebio/abt6_projects9/abt6_software/bin/reveal/env/bin/reveal", line 11, in <module> load_entry_point('reveal==0.1', 'console_scripts', 'reveal')() File "build/bdist.linux-x86_64/egg/reveal/reveal.py", line 294, in main File "build/bdist.linux-x86_64/egg/reveal/refine.py", line 44, in refine_bubble_cmd File "build/bdist.linux-x86_64/egg/reveal/refine.py", line 413, in refine_all File "build/bdist.linux-x86_64/egg/reveal/refine.py", line 206, in refine_bubble File "build/bdist.linux-x86_64/egg/reveal/refine.py", line 483, in msa2graph AttributeError: 'exceptions.OSError' object has no attribute 'output'

I've observed this behavior in different graphs with different maxsizes. and I'm not sure how this happens.

Cheers, Christian

jasperlinthorst commented 5 years ago

Hi Christian, For some reason subprocess raises an OSError while attempting to call 'muscle'. This exception isn't handled properly at the moment, which is something that I will fix. I can't really tell you why this OSError is raised, but I suspect that it has something to do with the fact that the exact command, something along the lines of: "muscle -in .fasta -quiet" on the concerning machine cannot the executed properly by the OS. As I think that this has something to do with your system configuration, it's a bit hard for me to help out with.

Good luck and let me know, Jasper

On Thu, Oct 4, 2018 at 10:21 AM ChriKub notifications@github.com wrote:

Hi, I'm using reveal realign with muscle to realign bubbles in a graph. reveal realign --64 --method muscle --all --maxsize 5000 -o $output $input At some point during the realignment it fails: 10/03/2018 01:04:06 PM Realigning bubble between <431323> and <99201>, 2 alleles, with muscle (max size 10bp, in nodes=2). Traceback (most recent call last): File "/ebio/abt6_projects9/abt6_software/bin/reveal/env/bin/reveal", line 11, in

load_entry_point('reveal==0.1', 'console_scripts', 'reveal')() File "build/bdist.linux-x86_64/egg/reveal/reveal.py", line 294, in main File "build/bdist.linux-x86_64/egg/reveal/refine.py", line 44, in refine_bubble_cmd File "build/bdist.linux-x86_64/egg/reveal/refine.py", line 413, in refine_all File "build/bdist.linux-x86_64/egg/reveal/refine.py", line 206, in refine_bubble File "build/bdist.linux-x86_64/egg/reveal/refine.py", line 483, in msa2graph AttributeError: 'exceptions.OSError' object has no attribute 'output' I've observed this behavior in different graphs with different maxsizes. and I'm not sure how this happens. Cheers, Christian — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub , or mute the thread .